suppressPackageStartupMessages({
library(Seurat)
library(cowplot)
library(ggplot2)
})
library(future)
plan("multiprocess", workers = 4)
options(future.globals.maxSize = 24000 * 1024^2)
# remove.packages("Matrix")
# packageurl <- "https://cran.r-project.org/src/contrib/Archive/Matrix/Matrix_1.3-2.tar.gz"
# install.packages(packageurl, repos=NULL, type="source")
alldata <- readRDS("../analysis/filtered_IMM_DN.rds")
DefaultAssay(alldata) = "RNA"
Find variable genes
suppressWarnings(suppressMessages(alldata <- FindVariableFeatures(alldata, selection.method = "vst",
nfeatures = 2000, verbose = FALSE, assay = "RNA")))
top20 <- head(VariableFeatures(alldata), 20)
LabelPoints(plot = VariableFeaturePlot(alldata), points = top20, repel = TRUE)

PCA
alldata <- RunPCA(alldata, npcs = 50, verbose = F)
plot_grid(ncol = 3,
DimPlot(alldata, reduction = "pca", group.by = "orig.ident", dims = 1:2) + NoLegend(),
DimPlot(alldata, reduction = "pca", group.by = "orig.ident", dims = 3:4) + NoLegend(),
DimPlot(alldata, reduction = "pca", group.by = "orig.ident", dims = 5:6) + NoLegend())

VizDimLoadings(alldata, dims = 1:5, reduction = "pca", ncol = 5, balanced = T)

ElbowPlot(alldata, reduction = "pca", ndims = 50)

Save data
saveRDS(alldata, file = "../analysis/filtered_IMM_DN_dr.rds")